rs10512425

Variant names:

• chr17-20720675-G-C
• rs10512425
• ENST00000441215.2:n.203+90G>C

Your query was ambiguous. Multiple possible variants found:

• chr17-20720675-G-C
• chr17-20720675-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441215.2(ENSG00000226521):​n.203+90G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0554 in 591,848 control chromosomes in the GnomAD database, including 1,053 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.051 (214 hom., cov: 31)
  • Exomes 𝑓: 0.057 (839 hom.)
• Consequence: ENSG00000226521 ENST00000441215.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.697
• Publications: 2 publications found

Genes affected

ENSG00000226521 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100287072	NR_172472.1	n.1262+90G>C		intron_variant	Intron 5 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226521	ENST00000441215.2	n.203+90G>C		intron_variant	Intron 2 of 10	6
ENSG00000290430	ENST00000578210.5	n.205+90G>C		intron_variant	Intron 2 of 5	2

Frequencies

GnomAD3 genomes AF: 0.0511 AC: 7779 AN: 152102 Hom.: 214 Cov.: 31

Gnomad AFR AF: 0.0355

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0704

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.0436

Gnomad FIN AF: 0.0443

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0612

Gnomad OTH AF: 0.0564

GnomAD4 exome AF: 0.0569 AC: 25003 AN: 439628 Hom.: 839 AF XY: 0.0559 AC XY: 13595 AN XY: 243304

African (AFR) AF: 0.0333 AC: 397 AN: 11930

American (AMR) AF: 0.0899 AC: 2833 AN: 31514

Ashkenazi Jewish (ASJ) AF: 0.0618 AC: 790 AN: 12788

East Asian (EAS) AF: 0.0158 AC: 390 AN: 24728

South Asian (SAS) AF: 0.0445 AC: 2625 AN: 59030

European-Finnish (FIN) AF: 0.0451 AC: 1667 AN: 36978

Middle Eastern (MID) AF: 0.0408 AC: 94 AN: 2302

European-Non Finnish (NFE) AF: 0.0632 AC: 15092 AN: 238882

Other (OTH) AF: 0.0519 AC: 1115 AN: 21476

GnomAD4 genome AF: 0.0511 AC: 7784 AN: 152220 Hom.: 214 Cov.: 31 AF XY: 0.0502 AC XY: 3737 AN XY: 74434

African (AFR) AF: 0.0356 AC: 1478 AN: 41536

American (AMR) AF: 0.0703 AC: 1075 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3472

East Asian (EAS) AF: 0.0141 AC: 73 AN: 5180

South Asian (SAS) AF: 0.0440 AC: 212 AN: 4816

European-Finnish (FIN) AF: 0.0443 AC: 470 AN: 10602

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0612 AC: 4161 AN: 68010

Other (OTH) AF: 0.0553 AC: 117 AN: 2116

Alfa AF: 0.0627 Hom.: 53

Bravo AF: 0.0514

Asia WGS AF: 0.0220 AC: 77 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	12
DANN	Benign	0.44
PhyloP100		0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10512425; hg19: chr17-20623988;